Merge branch 'develop'

Author: WardBrian

cmdstanpy/install_cmdstan.py

@@ -28,10 +28,9 @@
 from time import sleep
 from typing import Any, Callable, Dict, Optional
 
-from tqdm.auto import tqdm  # type: ignore
+from tqdm.auto import tqdm
 
 from cmdstanpy import _DOT_CMDSTAN, _DOT_CMDSTANPY
-
 from cmdstanpy.utils import (
     cmdstan_path,
     do_command,
@@ -94,7 +93,7 @@ def clean_all(verbose: bool = False) -> None:
         raise CmdStanInstallError(f'Command "make clean-all" failed\n{str(e)}')
 
 
-def build(verbose: bool = False, progress: bool = True) -> None:
+def build(verbose: bool = False, progress: bool = True, cores: int = 1) -> None:
     """
     Run command ``make build`` in the current directory, which must be
     the home directory of a CmdStan version (or GitHub repo).
@@ -107,8 +106,10 @@ def build(verbose: bool = False, progress: bool = True) -> None:
         Default is ``False``.
     :param progress: Boolean value; when ``True`` display progress progress bar.
         Default is ``True``.
+    :param cores: Integer, number of cores to use in the ``make`` command.
+        Default is 1 core.
     """
-    cmd = [MAKE, 'build']
+    cmd = [MAKE, 'build', f'-j{cores}']
     try:
         if verbose:
             do_command(cmd)
@@ -201,19 +202,26 @@ def compile_example(verbose: bool = False) -> None:
         raise CmdStanInstallError(f'Command "make clean-all" failed\n{e}')
 
 
-def rebuild_cmdstan(verbose: bool = False, progress: bool = True) -> None:
+def rebuild_cmdstan(
+    verbose: bool = False, progress: bool = True, cores: int = 1
+) -> None:
     """
     Rebuilds the existing CmdStan installation.
     This assumes CmdStan has already been installed,
     though it need not be installed via CmdStanPy for
     this function to work.
 
     :param verbose: Boolean value; when ``True``, show output from make command.
+        Default is ``False``.
+    :param progress: Boolean value; when ``True`` display progress progress bar.
+        Default is ``True``.
+    :param cores: Integer, number of cores to use in the ``make`` command.
+        Default is 1 core.
     """
     try:
         with pushd(cmdstan_path()):
             clean_all(verbose)
-            build(verbose, progress)
+            build(verbose, progress, cores)
             compile_example(verbose)
     except ValueError as e:
         raise CmdStanInstallError(
@@ -222,7 +230,11 @@ def rebuild_cmdstan(verbose: bool = False, progress: bool = True) -> None:
 
 
 def install_version(
-    cmdstan_version: str, overwrite: bool = False, verbose: bool = False
+    cmdstan_version: str,
+    overwrite: bool = False,
+    verbose: bool = False,
+    progress: bool = True,
+    cores: int = 1,
 ) -> None:
     """
     Build specified CmdStan version by spawning subprocesses to
@@ -245,7 +257,7 @@ def install_version(
             )
             clean_all(verbose)
             print('Rebuilding version {}'.format(cmdstan_version))
-        build(verbose)
+        build(verbose, progress=progress, cores=cores)
         print('Test model compilation')
         compile_example(verbose)
     print('Installed {}'.format(cmdstan_version))
@@ -418,6 +430,12 @@ def parse_cmdline_args() -> Dict[str, Any]:
         action='store_true',
         help="flag, when specified show progress bar for CmdStan download",
     )
+    parser.add_argument(
+        "--cores",
+        default=1,
+        type=int,
+        help="number of cores to use while building",
+    )
     if platform.system() == 'Windows':
         # use compiler installed with install_cxx_toolchain
         # Install a new compiler if compiler not found
@@ -520,6 +538,8 @@ def main(args: Dict[str, Any]) -> None:
                     cmdstan_version=cmdstan_version,
                     overwrite=args['overwrite'],
                     verbose=args['verbose'],
+                    progress=progress,
+                    cores=args['cores'],
                 )
             except RuntimeError as e:
                 print(e)

cmdstanpy/install_cxx_toolchain.py

@@ -303,11 +303,6 @@ def main(args: Dict[str, Any]) -> None:
 
     if 'progress' in args:
         progress = args['progress']
-        try:
-            # pylint: disable=unused-import
-            from tqdm import tqdm  # noqa: F401
-        except (ImportError, ModuleNotFoundError):
-            progress = False
     else:
         progress = False
 

cmdstanpy/model.py

@@ -14,7 +14,7 @@
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Mapping, Optional, Union
 
-from tqdm.auto import tqdm  # type: ignore
+from tqdm.auto import tqdm
 
 from cmdstanpy import _CMDSTAN_REFRESH, _CMDSTAN_SAMPLING, _CMDSTAN_WARMUP
 from cmdstanpy.cmdstan_args import (
@@ -1368,10 +1368,10 @@ def _run_cmdstan(
                     )  # make the typechecker happy
                     sampler_args.fixed_param = True
 
-    # pylint: disable=no-self-use
+    @staticmethod
     @progbar.wrap_callback
     def _wrap_sampler_progress_hook(
-        self, chain_id: int, total: int
+        chain_id: int, total: int
     ) -> Optional[Callable[[str], None]]:
         """Sets up tqdm callback for CmdStan sampler console msgs."""
         pbar: tqdm = tqdm(

cmdstanpy/utils.py

@@ -31,7 +31,7 @@
 import numpy as np
 import pandas as pd
 import ujson as json
-from tqdm.auto import tqdm  # type: ignore
+from tqdm.auto import tqdm
 
 from cmdstanpy import (
     _CMDSTAN_SAMPLING,
@@ -990,7 +990,7 @@ def do_command(
 
 
 def returncode_msg(retcode: int) -> str:
-    """ interpret retcode"""
+    """interpret retcode"""
     if retcode < 0:
         sig = -1 * retcode
         return f'terminated by signal {sig}'
@@ -1148,6 +1148,7 @@ def install_cmdstan(
     compiler: bool = False,
     progress: bool = False,
     verbose: bool = False,
+    cores: int = 1,
 ) -> bool:
     """
     Download and install a CmdStan release from GitHub. Downloads the release
@@ -1176,6 +1177,8 @@ def install_cmdstan(
     :param verbose: Boolean value; when ``True``, show console output from all
         intallation steps, i.e., download, build, and test CmdStan release.
         Default is ``False``.
+    :param cores: Integer, number of cores to use in the ``make`` command.
+        Default is 1 core.
 
     :return: Boolean value; ``True`` for success.
     """
@@ -1187,6 +1190,7 @@ def install_cmdstan(
         "compiler": compiler,
         "progress": progress,
         "dir": dir,
+        "cores": cores,
     }
 
     try:

pyproject.toml

@@ -20,7 +20,7 @@ warn_return_any = true
 
 [[tool.mypy.overrides]]
 module = [
-    'tqdm',
+    'tqdm.auto',
     'pandas',
     'ujson',
     'numpy', # these two are required for py36, which numpy 1.21 doesn't support

test/test_cmdstan_args.py

@@ -645,7 +645,6 @@ def test_args_fitted_params(self):
 class VariationalTest(unittest.TestCase):
     def test_args_variational(self):
         args = VariationalArgs()
-        self.assertTrue(True)
 
         args = VariationalArgs(output_samples=1)
         args.validate(chains=1)

test/test_model.py

@@ -9,7 +9,7 @@
 from testfixtures import LogCapture, StringComparison
 
 from cmdstanpy.model import CmdStanModel
-from cmdstanpy.utils import EXTENSION, cmdstan_path
+from cmdstanpy.utils import EXTENSION
 
 HERE = os.path.dirname(os.path.abspath(__file__))
 DATAFILES_PATH = os.path.join(HERE, 'data')
@@ -34,10 +34,6 @@
 
 
 class CmdStanModelTest(unittest.TestCase):
-    def show_cmdstan_version(self):
-        print('\n\nCmdStan version: {}\n\n'.format(cmdstan_path()))
-        self.assertTrue(True)
-
     def test_model_good(self):
         # compile on instantiation, override model name
         model = CmdStanModel(model_name='bern', stan_file=BERN_STAN)

test/test_variational.py

@@ -167,9 +167,6 @@ def test_variational_good(self):
 
         self.assertEqual(variational.variational_sample.shape, (1000, 5))
 
-    def test_variational_missing_args(self):
-        self.assertTrue(True)
-
     def test_variational_eta_small(self):
         stan = os.path.join(
             DATAFILES_PATH, 'variational', 'eta_should_be_small.stan'
@@ -186,7 +183,6 @@ def test_variational_eta_small(self):
         self.assertAlmostEqual(
             fabs(variational.variational_params_dict['mu[2]']), 0.09, places=1
         )
-        self.assertTrue(True)
 
     def test_variational_eta_fail(self):
         stan = os.path.join(